Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008606.1 Corchorus capsularis cultivar CVL-1 contig08627, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2694
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Found at i:360 original size:109 final size:108
Alignment explanation
Indices: 126--402 Score: 414
Period size: 109 Copynumber: 2.5 Consensus size: 108
116 ATAAAAAAAA
*
126 AATTATAAA-ATATT-GAATTTAATTAAATGAAAATAGAGTTTTTAGTAGAATAAAATTGTATAT
1 AATTATAAAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAATTGTATAT
189 TAGAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
65 TAGAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
* *
233 AATTATACAGATATTAGATTTAATTAAATGAAAATTGAGTTTTTAGTAAAATAAAATTGTATATT
1 AATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAATTGTATATT
*
298 AGAAAAAATTTTAGTATATCCAAATTTTTTGGTAAAAATAAAGT
66 AG-AAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
* * *
342 AATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAA
1 AATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTAGTAAAATAAAA
403 CTATAATAGT
Statistics
Matches: 153, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
107 8 0.05
108 53 0.35
109 63 0.41
110 2 0.01
111 1 0.01
114 26 0.17
ACGTcount: A:0.48, C:0.02, G:0.11, T:0.39
Consensus pattern (108 bp):
AATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAATTGTATATT
AGAAAAATTTTAATATATCCAAATTTTTTGGTAAAAATAAAGT
Found at i:697 original size:5 final size:5
Alignment explanation
Indices: 684--715 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
674 GGGGTTGATC
*
684 TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
716 GAGTTAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:1781 original size:178 final size:177
Alignment explanation
Indices: 1458--1893 Score: 504
Period size: 178 Copynumber: 2.4 Consensus size: 177
1448 TTTTCGGTAT
* * ** * *
1458 TTGAAAAATCAAATTTAGCTTTCAAGTCCTACATGAAAGTTGAAGATCATGAAACAGCCTTTTAA
1 TTGAAACATTAAATTTAGCTTTTGAGTCCTACATGAAAGTTGTAGATCATGAAACAACCTTTT-A
* * * *** * * *
1523 CAGACACTTAAATCATCTCAATCGGACATCTAGAGCAAAAATAATGTATTATTTAGTAGACCGTT
65 TAGACACTTGAATCAGCTCAAGAAGACATCTAGACCAAAAATAATGTATTATTAAGTAGACCGTC
* *
1588 CATTCTCGCTAACCGAAAAAATTAAATT-TTTGGAAGCATTTTTT-ATAC
130 CATTCTCGCTAACCGAAAAAACT-AATTATTCGGAAGC-TTTTTTGATAC
* * * * *
1636 TTGAAACGTTAAATTTAGCTTTTGCGTCCTACATGAAAGTTGTAGATAATAAAATAACCTTTTAT
1 TTGAAACATTAAATTTAGCTTTTGAGTCCTACATGAAAGTTGTAGATCATGAAACAACCTTTTAT
* * * *
1701 GAGACACTTGAATCAGCTCAAGAAGACATCTGGACCAAAAGTAATGT-TATATTAAGTGGATCGT
66 -AGACACTTGAATCAGCTCAAGAAGACATCTAGACCAAAAATAATGTAT-TATTAAGTAGACCGT
* *
1765 CCATT-TCCGTTAACCGAAACAACTAATTATTCGGAAGCTTTTTTGATAC
129 CCATTCT-CGCTAACCGAAAAAACTAATTATTCGGAAGCTTTTTTGATAC
*
1814 TTGAAACATTAAATTTAG-TTTTCGAGTCTTACATGAAAGTTGTAGATCATGAAACAACCTTTTA
1 TTGAAACATTAAATTTAGCTTTT-GAGTCCTACATGAAAGTTGTAGATCATGAAACAACCTTTT-
1878 ATAGACACTTGAATCA
64 ATAGACACTTGAATCA
1894 TCTTGATCGG
Statistics
Matches: 217, Mismatches: 34, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
177 17 0.08
178 198 0.91
179 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (177 bp):
TTGAAACATTAAATTTAGCTTTTGAGTCCTACATGAAAGTTGTAGATCATGAAACAACCTTTTAT
AGACACTTGAATCAGCTCAAGAAGACATCTAGACCAAAAATAATGTATTATTAAGTAGACCGTCC
ATTCTCGCTAACCGAAAAAACTAATTATTCGGAAGCTTTTTTGATAC
Done.